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This dashboard summarises analysis of one microsecond molecular dynamics simulations of five conditions:

1. 3VRI, HLA-B*57:01-RVAQLENVYI in complex with abacavir
2. 3VRI, minus peptide
3. 3VRI, minus abacavir
4. 2RFX, HLA-B*5701, presenting the self peptide, LSSPVTKSF
5. 2RFX, minus peptide

The summary dashboard shows:

• Pictures of the two different abacavir conformations observed in condition 2.
• PCA A: The conformational landscapes defined by the major collective motions, these are the contour plots indicating how many distinct populations were observed during 1 microsecond simulations. (The motions were calculated using C-alpha atoms only).
• PCA A: Graphs of the extent of each of the first 20 major motion contribution to the overall motions i.e. the percentage of variance.
• PCA B: Animations of the top two collective motions PC1 and PC2, together accounting for around 50% of total motions in each case.
• Residue Flexibility: Graphs of the residue root mean square fluctuations i.e. how much each residue moved relative to its average position, and therefore a measure of the relative flexibility of each residue in the protein under each condition.

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3VRI no peptide initial abacavir conformation

3VRI no peptide flipped abacavir conformation

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The top two major collective motions, left to right:

3VRI, HLA-B57:01-RVAQLENVYI in complex with abacavir. 3VRI, minus peptide. 3VRI, minus abacavir. 2RFX, HLA-B57:01-LSSPVTKSF. 2RFX, minus peptide.

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